This study hypothesizes that the combination of atovaquone/azithromycin will be equivalent to or superior to trimethoprim/sulfamethoxazole for the prevention of serious bacterial infection in HIV-infected children with depleted CD4 lymphocyte populations. After stratifying for previous use of TMP/SMX and/or IVIG, subjects are randomized to one of two arms: TMP/SMX (5 mg/kg/day) or micronized atovaquone (30 mg/kg/day) plus azithromycin (5 mg/kg/day). Cross-over to the alternative drug regimen will occur if a serious treatment-related toxicity is observed. The efficacy of the antibacterial regimens is being evaluated through monitoring the occurrence of serious bacterial infections or PCP break-through. Subjects will receive study drug until the last subject enrolled has completed 3 years or when there are 530, 475, and 420 subjects who have been followed for one, two and three years, respectively. The first 30 subjects were to have had a pharmacokinetics profile performed to assist in insuring that previously established blood concentrations of azithromycin and atovaquone were not significantly affected by the administration of the two drugs in combination.